fix: address sixth round of Copilot PR review feedback

- Validate {CORE_TEMPLATE} placeholder in bash wrap strategy: fail
  with clear error if placeholder is missing in wrapper content
- Validate {CORE_TEMPLATE} placeholder in PowerShell wrap strategy:
  throw if placeholder is missing, matching Python resolver behavior
- Fix PowerShell pyCmd arg slicing: build extra-args array based on
  actual Count to avoid out-of-range $null arguments
- Narrow exception catch in _register_for_non_skill_agents(): catch
  only ValueError instead of broad Exception
- Add _reconcile_skills() post-removal: re-register SKILL.md files
  from the next winning preset so skills stay in sync with the
  effective command stack after removing a top-priority preset

Author: mnriem

scripts/bash/common.sh

@@ -543,7 +543,12 @@ except Exception:
                     prepend) content="$(printf '%s\n\n%s' "$layer_content" "$content")" ;;
                     append)  content="$(printf '%s\n\n%s' "$content" "$layer_content")" ;;
                     wrap)
-                        # Split on placeholder and rejoin with content to avoid
+                        # Validate placeholder exists
+                        case "$layer_content" in
+                            *'{CORE_TEMPLATE}'*) ;;
+                            *) echo "Error: wrap strategy missing {CORE_TEMPLATE} placeholder" >&2; return 1 ;;
+                        esac
+                        # Split on first placeholder and rejoin with content to avoid
                         # bash & expansion in parameter substitution replacement.
                         local before="${layer_content%%\{CORE_TEMPLATE\}*}"
                         local after="${layer_content#*\{CORE_TEMPLATE\}}"
@@ -557,6 +562,10 @@ except Exception:
                 prepend) content="$(printf '%s\n\n%s' "$layer_content" "$content")" ;;
                 append)  content="$(printf '%s\n\n%s' "$content" "$layer_content")" ;;
                 wrap)
+                    case "$layer_content" in
+                        *'{CORE_TEMPLATE}'*) ;;
+                        *) echo "Error: wrap strategy missing {CORE_TEMPLATE} placeholder" >&2; return 1 ;;
+                    esac
                     local before="${layer_content%%\{CORE_TEMPLATE\}*}"
                     local after="${layer_content#*\{CORE_TEMPLATE\}}"
                     content="${before}${content}${after}"

scripts/powershell/common.ps1

@@ -420,7 +420,8 @@ function Resolve-TemplateContent {
                 if ((Test-Path $manifest) -and $pyCmd) {
                     try {
                         # Use Python to parse YAML manifest for strategy and file path
-                        $stratResult = & $pyCmd[0] @($pyCmd[1..99]) -c @"
+                        $pyArgs = if ($pyCmd.Count -gt 1) { $pyCmd[1..($pyCmd.Count-1)] } else { @() }
+                        $stratResult = & $pyCmd[0] @pyArgs -c @"
 import sys
 try:
     import yaml
@@ -524,15 +525,25 @@ except Exception:
                 switch ($strat) {
                     'prepend' { $content = "$layerContent`n`n$content" }
                     'append'  { $content = "$content`n`n$layerContent" }
-                    'wrap'    { $content = $layerContent.Replace('{CORE_TEMPLATE}', $content) }
+                    'wrap'    {
+                        if (-not $layerContent.Contains('{CORE_TEMPLATE}')) {
+                            throw "Wrap strategy missing {CORE_TEMPLATE} placeholder"
+                        }
+                        $content = $layerContent.Replace('{CORE_TEMPLATE}', $content)
+                    }
                 }
             }
         } else {
             switch ($strat) {
                 'replace' { $content = $layerContent }
                 'prepend' { $content = "$layerContent`n`n$content" }
                 'append'  { $content = "$content`n`n$layerContent" }
-                'wrap'    { $content = $layerContent.Replace('{CORE_TEMPLATE}', $content) }
+                'wrap'    {
+                    if (-not $layerContent.Contains('{CORE_TEMPLATE}')) {
+                        throw "Wrap strategy missing {CORE_TEMPLATE} placeholder"
+                    }
+                    $content = $layerContent.Replace('{CORE_TEMPLATE}', $content)
+                }
             }
         }
     }

src/specify_cli/presets.py

@@ -747,9 +747,42 @@ def _register_for_non_skill_agents(
                         agent_name, commands, source_id,
                         source_dir, self.project_root,
                     )
-                except (ValueError, Exception):
+                except ValueError:
                     continue
 
+    def _reconcile_skills(self, command_names: List[str]) -> None:
+        """Re-register skills for commands whose winning layer changed.
+
+        After a preset is removed, finds the next preset in the priority
+        stack that provides each command and re-runs skill registration
+        for that preset so SKILL.md files reflect the current winner.
+
+        Args:
+            command_names: List of command names to reconcile skills for
+        """
+        if not command_names:
+            return
+
+        resolver = PresetResolver(self.project_root)
+        for cmd_name in command_names:
+            layers = resolver._collect_all_layers(cmd_name, "command")
+            if not layers:
+                continue
+
+            top_path = layers[0]["path"]
+            # Find the preset that owns the winning layer
+            for pack_id, _meta in PresetRegistry(self.presets_dir).list_by_priority():
+                pack_dir = self.presets_dir / pack_id
+                if top_path.is_relative_to(pack_dir):
+                    manifest_path = pack_dir / "preset.yml"
+                    if manifest_path.exists():
+                        try:
+                            manifest = PresetManifest(manifest_path)
+                        except PresetValidationError:
+                            break
+                        self._register_skills(manifest, pack_dir)
+                    break
+
     def _get_skills_dir(self) -> Optional[Path]:
         """Return the active skills directory for preset skill overrides.
 
@@ -1326,6 +1359,9 @@ def remove(self, pack_id: str) -> bool:
         # re-resolve from the remaining stack so the next layer takes effect.
         if removed_cmd_names:
             self._reconcile_composed_commands(list(removed_cmd_names))
+            # Also reconcile skills so SKILL.md files reflect the new winning
+            # command layer rather than being left absent or stale.
+            self._reconcile_skills(list(removed_cmd_names))
 
         return True